AESOP is a Python 2.7 library, and is not compatible with Python 3.

Anaconda installation

We recommend installing the Anaconda Python Distribution as it comes with several packages used by AESOP pre-installed. Anaconda can be downloaded from here. If you choose this route, install Anaconda2. Anaconda3 is not compatible with AESOP.


The 64-bit version is recommended for Linux, Mac OS, and Windows. To install ProDy in 64-bit windows, you can use an installer from PyPI. If you have issues with a 64-bit installation, AESOP should be compatible with a 32-bit Python installation, though it is not as well tested.

Install PDB2PQR, APBS and Coulomb

Please download and install the appropriate version of PDB2PQR and APBS (Coulomb installs alongside APBS) for your operating system. Ensure that the executables are added to your path by running the executable in terminal/command prompt:




Linux users: Add the directories containing the apbs, pdb2pqr, and coulomb executables to path in your ~/.profile. As an example:

export PATH=/opt/pdb2pqr-linux-bin64-2.1.0:$PATH
export PATH=/opt/APBS-$PATH
export PATH=/opt/APBS-$PATH

You may encounter issues with PDB2PQR if you are using an older version that uses the script. In this case, either update to a newer binary PDB2PQR distribution, or specify the full path to in AESOP.

Mac users: If you are using the APBS binary/executable to install (as opposed to compiling from source), you may need to add the following line to your path:

export PATH=$PATH:`dirname '/Applications/'`

Then you may add the pdb2pqr executable to path as in the Linux case

Windows users: Navigate to system settings (Control panel > System and Security > System) and click advanced settings. Select the environment variables box and edit the Path variable for the system or for the user. Append the paths to the directories containing the apbs, pdb2pqr, and coulomb executables (each as a separate entry in the Path variable).

Install other dependencies


pip install prody


If pip is unable to install prody (which is likely to happen if you are running a Windows operating system), then you may download installation materials appropriate for your OS directly from the PyPI website. For Windows, it is typically easier to use the appropriate installation executable appropriate for your Python 2.7 installation (choose amd64 for 64-bit Python 2.7 and choose win32 for 32-bit Python 2.7). As a reminder, AESOP is only compatible with Python 2.7.


conda config --add channels salilab
conda install modeller


Modeller will require users to have a license key. Registration is located at the Sali Lab Website. The Modeller license key will be used in the following manner:

Edit //anaconda/lib/modeller-9.17/modlib/modeller/ and replace XXXX with your Modeller license key (or set the KEY_MODELLER environment variable before running ‘conda install’).

Multiprocessing (optional):

pip install multiprocessing


Multiprocessing is only needed if you are planning to utilize multiple cores in your analysis.

NetworkX (optional):

conda install networkx


NetworkX is only required for the plotNetwork utility.

Plotly (optional):

pip install plotly


Plotly is only required for the interactive plotting functions such as plotScan_interactive, plotNetwork_interactive, and plotESD_interactive.

Installing AESOP

You can install AESOP from PyPi using:

pip install aesop

If you already have it installed, you can upgrade to the latest version using:

pip install --upgrade aesop

If you are having issues installing through PyPi, you may try to Install from source.

Install from source

To install from source, you can use the following commands to clone the GitHub repository and install manually:

git clone
cd aesop-python
pip install


This may require administrative privileges.